Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private tutor.
sagar barage wrote:
Dear sir,
when i was done the MD of crystal structure the both nitrogen
of immadazol ring of histidine is protonated
which are not protonated in crystal structure.
There are no protons in crystal structures.
all histidine in structure contain single protonation but some
Histidine is double protonated at both nitrogen
why this happens in gromacs?
Please read the manual information (or pdb2gmx -h) about how pdb2gmx attempts to
add hydrogens to the input structure.
-Justingm
--
Sagar H. Barage
[email protected] <mailto:[email protected]>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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